Spontaneous tumors often contain heterogeneous populations of tumor cells with different tumor-initiating potentials or cancer cell "stemness." Clonal heterogeneity can be traced to specific locations inside a tumor where clones with different metastatic capabilities are identified, suggesting that the tumor microenvironment can exert a significant effect on the evolution of different clonal populations. Hypoxia is a common feature of tumor microenvironments and has the potential to facilitate malignant progression. This chapter provides a synopsis of hypoxia-regulated pathways implicated in the maintenance of cancer stem cells.